Tokyo is one of the world's safest major cities. Violent crime is extraordinarily rare. Lost items are regularly turned in to koban (police boxes). The main practical concern is navigating the train system — get a Suica or Pasmo IC card immediately upon arrival for seamless transit.
Natural hazard awareness is important: Tokyo sits in an earthquake zone. All hotels have emergency instructions. Download the Tokyo Bosai (disaster prevention) app. Typhoon season is August–September. Otherwise, solo travelers of all genders report feeling completely safe at all hours throughout the city.